What about Windows OS with Microsoft ad or drinking a Coke with a Coke ad on the can or driving a Honda/Ford/etc with it's ad on the side/back? Whiney.
1) Haven't played it yet, but I've read there are positives and negatives to your choices but they aren't immediate like most other games. You may not see the effects of a choice for hours.
2) Also goes with 1. I wouldn't worry about missing things. Just play however you want the first...